[Matplotlib-users] 3rd y-axis in plot

[philscher]

Hello,

I need to plot 3 functions into the same plot, each having different scales
(same x, different y values).
For the first 2 functions I can use twinx(). But how can I include a 3rd
axis, which should appear
beside the first y-axis and plot the 3rd function ? 

Thanks for matplotlib & help

Paul
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[Matplotlib-users] SpanSelector on multiple figures

[justfred]

Hi,

I'm wondering if it is possible to use SpanSelector on multiple figures : my
problem is that I can't think of a way to tell the onselect on which
axes(ses) of which figure it should try and do something. The example works
because there is only one SpanSelector active and "it" therefore knows which
axes "it" should redraw.

For it to work on multiple figures (say I have a series of events that I
plot in a similar way each in a separate figure and I would like a
SpanSelector feature on each of the figures) I would need to have a
reference to which axes called the onselect through SpanSelector : then I
could get the axes's figure and manipulate the other subplots on that figure
accordingly.

Is there a way of doing this ?

Kind regards,
Frederic

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[Matplotlib-users] Hardcoded DPI settings in PDF and Cairo backends

[David Kiliani]

Hi,

I'm currently doing my diploma thesis with matplotlib plots and I have a
problem there. Many of the plots include an imshow(), which is completly
blurred when I do a savefig() to PDF. The problem seems to be the
hardcoded DPI settings in the PDF and Cairo backends (dpi=72), which is
far too low for a printing quality image. When looking for the source of
this setting, I found
http://matplotlib.svn.sourceforge.net/viewvc/matplotlib?view=rev&revision=4933
which does not make any sense to me. Why was the kwargs readout
disabled, even if the default setting was already 72dpi? If I
explicitely do a savefig(file, dpi=XX), it could be assumed that I
REALLY WANT a DPI setting of XX. And if I don't supply any dpi
parameter, the default of 72 will be used.

Best regards,
David




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[Matplotlib-users] Animation with copy_from_bbox / restore_region.

[Elan Pavlov]

Hi,

I'm trying to use matplotlib for animating data as it is received from an 
online source (online in the algorithmic sense not internet:). I'd like 
the graph plot to be updated with high frequency since the data changes 
rapidly. I've used the BufferRegion with copy_from_bbox / restore_region 
and it speeds up the plotting considerably but alas it's still not good 
enough (with a large number of graphs and a large number of data points in 
each graph).

What I'd like to do is to utilize the fact that the animation is updated 
in a predictable fashion (i.e., scrolling off the screen to the left as 
new data arrives) in order to speed up the animation. The idea would be to 
copy the right 99% of the graph (or some other fraction) via some kind of 
function similar to copy_from_bbox, move it 1% to the left and then plot 
the new 1% of the data. The problem is that as far as I can tell the 
copy_from_bbox/restore_region does not actually allow changing the area in 
which it is restored. I've mucked around in the source files a bit but to 
no avail.

My question is then:
1. Is there some other way to copy everything enclosed in a Bbox? or
2. Is there some way to modify the region in which data reappears when 
using restore_region?
3. Perhaps I'm missing something?

I'm sure someone else has done this since it seems pretty natural and 
useful for a variety of applications.

Elan

"If stupidity got us into this mess, why can't it get us out?"
- Will Rogers

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[Matplotlib-users] SpanSelector on multiple figures

[fjldurodie]

Hi,

I'm wondering if it is possible to use SpanSelector on multiple figures 
: my problem is that I can't think of a way to tell the onselect on 
which axes(ses) of which figure it should try and do something. The 
example works because there is only one SpanSelector active and "it" 
therefore knows which axes "it" should redraw.

For it to work on multiple figures (say I have a series of events that I 
plot in a similar way each in a separate figure and I would like a 
SpanSelector feature on each of the figures) I would need to have a 
reference to which axes called the onselect through SpanSelector : then 
I could get the axes's figure and manipulate the other subplots on that 
figure accordingly.

Is there a way of doing this ?

Kind regards,
Frederic

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[Matplotlib-users] Matplotlib running under cron

[olslewfoot]

I have been successfully producing graphics as pngs with matplotlib and
running them as cron jobs with Linux for some time. These graphics used
"standard" colors.

I recently changed some of the colours, using tuples of RGB values instead
of the standard colors and now the scripts will run from the command line,
but not as scheduled cron jobs and I get the following error:

Unable to access the X Display, is $DISPLAY set properly?

The script then terminates.

Can anyone help me with how to set the display in cron and run Matplotlib
as a cron job.

Thanks
John

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[Matplotlib-users] Matplotlib running under cron

[john . bacon]

I have been successfully producing graphics as pngs with matplotlib and
running them as cron jobs with Linux for some time. These graphics used
"standard" colors.

I recently changed some of the colours, using tuples of RGB values instead
of the standard colors and now the scripts will run from the command line,
but not as scheduled cron jobs and I get the following error:

Unable to access the X Display, is $DISPLAY set properly?

The script then terminates.

Can anyone help me with how to set the display in cron and run Matplotlib
as a cron job.

Thanks
John


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Re: [Matplotlib-users] Matplotlib running under cron

[Michael Droettboom]

This is usually caused by having an interactive backend (such as Gtk, 
Qt, Tk) which would require X11.  Try setting your backend to "Agg".

  import matplotlib
  matplotlib.use("Agg")

Cheers,
Mike

john.ba...@worstead.co.uk wrote:
> I have been successfully producing graphics as pngs with matplotlib and
> running them as cron jobs with Linux for some time. These graphics used
> "standard" colors.
>
> I recently changed some of the colours, using tuples of RGB values instead
> of the standard colors and now the scripts will run from the command line,
> but not as scheduled cron jobs and I get the following error:
>
> Unable to access the X Display, is $DISPLAY set properly?
>
> The script then terminates.
>
> Can anyone help me with how to set the display in cron and run Matplotlib
> as a cron job.
>
> Thanks
> John
>
>
> --
> Stay on top of everything new and different, both inside and 
> around Java (TM) technology - register by April 22, and save
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>   

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Re: [Matplotlib-users] does matplotlib install work???

[Michael Droettboom]

Can you provide more information, such as any messages emitted when you 
import pylab?

John Seales wrote:
>
>
> 
> From: praxbaf...@hotmail.com
> To: matplotlib-users@lists.sourceforge.net
> Date: Tue, 21 Apr 2009 16:14:37 -0700
> Subject: [Matplotlib-users] help installing matplotlib
>
> I have an intel mac running os 10.4.11. I use python 2.6
>
> When I install matplotlib it seems to work, but then there is a bug 
> about pylab. There is a font that doesn't work.
>
> Can anybody out there help me?
>
>
>
> 
> Windows Live™ Hotmail®:…more than just e-mail. Check it out. 
> 
> 
> Rediscover Hotmail®: Get e-mail storage that grows with you. Check it 
> out. 
> 
>  
>
> 
>
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Re: [Matplotlib-users] prevent clipping?

[Michael Droettboom]

You can call "set_clip_box(None)" on all of the artists you draw.  (The 
circles and other patches etc.)

Cheers,
Mike

Carlos Guâno Grohmann wrote:
> Dears,
>
> In this app I'm working on, I have a circular plot (not a polar plot,
> just a plot inside a circular area) in a panel, within a
> wx.splitterwindow.
> The problem is that the edges of the plot are being clipped (see
> screenshots). How to prevent this from happening? I tried different
> combination of aces.set_xlim() and axes.set_xbound(), but without
> success (I also don't the difference between xlim and xbound).
>
> screenshots , code  and sample data attached.
>
> many thanks
>
>
>
>   
> 
>
> 
>
> 
>
> 
>
> 
>
> 
>
> --
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[Matplotlib-users] set fixed xrange

[Till Backhaus]

Hi there,

I'm using matplotlib (version 0.98.5.2) to generate a couple of bar- 
charts for a website.
Until now I've not been able to find a way set the x axis to a fixed  
range.

Suppose my data is turnover per hour. Now: If there is zero turnover  
at the beginning
or the end of a period matplotlib omits that value and limits the  
xrange so that non-zero
hours reside on the edges which would be confusing for the users.

This is the code:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(5,4),dpi=72)
ax = fig.add_subplot(111)
ax.set_ylabel('EUR')
ax.set_xlabel('Hour')
ax.set_xlim((1,24))
ax.bar(data.keys(),data.values(),width=1,align='center')
fig.savefig(filename)

I searched the docs but I didn't find anything that could fix my  
problem.
It would be great if anybody knew (and told me) what I am doing wrong.

Thanks in advance

Till Backhaus

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Re: [Matplotlib-users] Matplotlib running under cron

[Jouni K . Seppänen]

john.ba...@worstead.co.uk writes:

> I recently changed some of the colours, using tuples of RGB values instead
> of the standard colors and now the scripts will run from the command line,
> but not as scheduled cron jobs and I get the following error:
>
> Unable to access the X Display, is $DISPLAY set properly?

This has probably nothing to do with the way you specify colors. For
some reason matplotlib is using an interactive backend. Make sure that
your script starts with

import matplotlib
matplotlib.use('Agg')

or that you specify the Agg backend in your matplotlibrc file.

-- 
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Re: [Matplotlib-users] Hardcoded DPI settings in PDF and Cairo backends

[Jouni K . Seppänen]

David Kiliani  writes:

> http://matplotlib.svn.sourceforge.net/viewvc/matplotlib?view=rev&revision=4933
> which does not make any sense to me. Why was the kwargs readout
> disabled, even if the default setting was already 72dpi?

Before that change, the dpi setting changed the size of the pages
produced by the pdf backend, not the resolution. But since revision 6645
(release version 0.98.5.2) the dpi argument should set the resolution
of images again. (I think this used to work before the Great Transform
Refactoring, so in versions on the 0.91 branch it should work, too.)

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Re: [Matplotlib-users] savefig bug

[Michael Droettboom]

I think Jae-Joon's assesment is correct, since the logical dpi in PS is 
hardcoded to 72.0.  I have made this change in the SVN repository.

Mike

Thomas Robitaille wrote:
> Thanks for your quick reply!
>
> I'll be patient and wait for the fix to be made in the SVN repository,  
> rather than trying to patch it myself. Do I need to add any  
> information to the bug report?
>
> Best,
>
> Thomas
>
> On Apr 21, 2009, at 1:06 PM, Jae-Joon Lee wrote:
>
>   
>> I can reproduce this bug with the current svn.
>>
>> It works correctly If you set dpi=72, but it seems that it would not
>> be an option in your case.
>>
>> It seems to me that this is related with the change in r6847 that  
>> Michael made.
>>
>> http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/matplotlib/lib/matplotlib/backends/backend_ps.py?r1=6734&r2=6847
>>
>> At line 431 of the backend_ps.py,
>>
>> clip = (0.0, 0.0, self.width * self.imagedpi,
>>   self.height * self.imagedpi)
>>
>> I think we should use the dpi of the figure, instead of the imagedpi
>> of the renderer.
>> Replacing self.imagedpi with 72 (which is the dpi of the figure when
>> ps backend is used) seems to solve the problem.
>>
>> Thomas, I don't see any easy workaround for this bug other than
>> patching the code. Others may have better insight though.
>>
>> Regards,
>>
>> -JJ
>>
>>
>>
>> On Tue, Apr 21, 2009 at 9:59 AM, Thomas Robitaille
>>  wrote:
>> 
>>> Hi,
>>>
>>> I've come across a bug with the savefig method when using the dpi=
>>> argument and saving an EPS file. If you try the following code, you
>>> will see that the frame is incomplete. Is there a way to solve this
>>> from a user point of view?
>>>
>>> ---
>>>
>>> import matplotlib
>>> matplotlib.use('Agg')
>>> from matplotlib.pyplot import *
>>>
>>> import numpy as np
>>>
>>> nx,ny = 10,10
>>>
>>> image = np.random.random((nx,ny))
>>>
>>> fig = figure(figsize=(4,4))
>>> ax = fig.add_subplot(111)
>>> ax.imshow(image,interpolation='nearest')
>>> fig.savefig('plot.eps',dpi=30)
>>>
>>> ---
>>>
>>> I've submitted a bug report:
>>>
>>> https://sourceforge.net/tracker/?func=detail&aid=2777476&group_id=80706&atid=560720
>>>
>>> Thanks,
>>>
>>> Thomas
>>>
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>>>   
>
>
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Re: [Matplotlib-users] set fixed xrange

[Ryan May]

On Thu, Apr 23, 2009 at 8:40 AM, Till Backhaus  wrote:

> Hi there,
>
> I'm using matplotlib (version 0.98.5.2) to generate a couple of bar-
> charts for a website.
> Until now I've not been able to find a way set the x axis to a fixed
> range.
>
> Suppose my data is turnover per hour. Now: If there is zero turnover
> at the beginning
> or the end of a period matplotlib omits that value and limits the
> xrange so that non-zero
> hours reside on the edges which would be confusing for the users.
>
> This is the code:
> import matplotlib
> matplotlib.use('Agg')
> import matplotlib.pyplot as plt
> fig = plt.figure(figsize=(5,4),dpi=72)
> ax = fig.add_subplot(111)
> ax.set_ylabel('EUR')
> ax.set_xlabel('Hour')
> ax.set_xlim((1,24))
> ax.bar(data.keys(),data.values(),width=1,align='center')
> fig.savefig(filename)
>

Try moving the call to ax.set_xlim to *after* the call to ax.bar.

Ryan

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Re: [Matplotlib-users] SpanSelector on multiple figures

[Jae-Joon Lee]

On Mon, Apr 20, 2009 at 4:09 PM, fjldurodie
 wrote:
> Hi,
>
> I'm wondering if it is possible to use SpanSelector on multiple figures
> : my problem is that I can't think of a way to tell the onselect on
> which axes(ses) of which figure it should try and do something. The
> example works because there is only one SpanSelector active and "it"
> therefore knows which axes "it" should redraw.
>
> For it to work on multiple figures (say I have a series of events that I
> plot in a similar way each in a separate figure and I would like a
> SpanSelector feature on each of the figures) I would need to have a
> reference to which axes called the onselect through SpanSelector : then
> I could get the axes's figure and manipulate the other subplots on that
> figure accordingly.

Mouse event in mpl has a "inaxes" property. However, SpanSelector hide
event information from users.

On the other hand, the first argument of the SpanSelector is the
"axes" that you want to use. So, I'm not sure what your point is. You
already know the axes you're working with. Can't you just use
different callbacks for different axes?

-JJ


>
> Is there a way of doing this ?
>
> Kind regards,
> Frederic
>
> --
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
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Re: [Matplotlib-users] pylab quick reference? (

[Esmail]

Selam to you too Gökhan,

Gökhan SEVER wrote:
> 
> What I recommend you is: watching John Hunter's video at Matplotlib by 
> John D. Hunter . His 
> introduction of matplotlib and examples he use could be very interesting 
> to watch for you.

I just started to check out the video, looks interesting and useful,
thanks for the link.

> Also you can take a look at this book: Beginning Python Visualization: 
> Crafting Visual Transformation Scripts

I had not heard of this book before, I'll look for more information
on it.

> Good luck on your plotting adventures.

Thanks - it's fun to learn new things.

Cheers,
Esmail


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Re: [Matplotlib-users] pylab quick reference? (

[Esmail]

  > There is no quick reference, though one would be handy.  If you scroll
> down to the bottom of the main page at
> 
> http://matplotlib.sourceforge.net/index.html
> 
> there is a summary of the pyplot plotting commands with links to the 
> full docs.  You can at least see most everything that is available in 
> pyplot in one place. 
> 
> JDH


ah .. nice, thanks!

Esmail


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Re: [Matplotlib-users] Animation with copy_from_bbox / restore_region.

[Jae-Joon Lee]

On Mon, Apr 20, 2009 at 4:34 PM, Elan Pavlov  wrote:
> Hi,
>
> I'm trying to use matplotlib for animating data as it is received from an
> online source (online in the algorithmic sense not internet:). I'd like
> the graph plot to be updated with high frequency since the data changes
> rapidly. I've used the BufferRegion with copy_from_bbox / restore_region
> and it speeds up the plotting considerably but alas it's still not good
> enough (with a large number of graphs and a large number of data points in
> each graph).
>

Well, if you need your plot updated with very high frequency, MPL may
not be your tool of choice.
Anyhow, my first recommendation is not to update the plot frequently.
I mean, do you have to update the plot for every changes? Can you
update it every 10th change, for example?

> What I'd like to do is to utilize the fact that the animation is updated
> in a predictable fashion (i.e., scrolling off the screen to the left as
> new data arrives) in order to speed up the animation. The idea would be to
> copy the right 99% of the graph (or some other fraction) via some kind of
> function similar to copy_from_bbox, move it 1% to the left and then plot
> the new 1% of the data. The problem is that as far as I can tell the
> copy_from_bbox/restore_region does not actually allow changing the area in
> which it is restored. I've mucked around in the source files a bit but to
> no avail.
>
> My question is then:
> 1. Is there some other way to copy everything enclosed in a Bbox? or
> 2. Is there some way to modify the region in which data reappears when
> using restore_region?
> 3. Perhaps I'm missing something?
>
> I'm sure someone else has done this since it seems pretty natural and
> useful for a variety of applications.

I'm attaching a patch that might do what you want to do.
It implements a "restore_bbox2" method which restores a subset of the
saved background at a specified position.
A small example is also attached (it is based on the gtk backend).

I, personally, am not sure if this kind of feature is useful. If you
shift part of your figure, you have to be careful not to mess up with
the coordinate system. And also be careful about what to be shifted
and what to be not (e.g., ticks).

If others find this useful, I'll commit this to the trunk with some
api improvement.

Regards,

-JJ


>
> Elan
> 
> "If stupidity got us into this mess, why can't it get us out?"
>        - Will Rogers
>
> --
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>
Index: src/_backend_agg.cpp
===
--- src/_backend_agg.cpp	(revision 7061)
+++ src/_backend_agg.cpp	(working copy)
@@ -104,6 +104,18 @@
 return Py::Object();
 }
 
+Py::Object BufferRegion::get_bounds(const Py::Tuple &args) {
+args.verify_length(0);
+
+Py::Tuple bounds(4);
+bounds[0] = Py::Int(rect.x1);
+bounds[1] = Py::Int(rect.y1);
+bounds[2] = Py::Int(rect.x2);
+bounds[3] = Py::Int(rect.y2);
+
+return bounds;
+}
+
 Py::Object BufferRegion::to_string_argb(const Py::Tuple &args) {
   // owned=true to prevent memory leak
   Py_ssize_t length;
@@ -426,6 +438,54 @@
   return Py::Object();
 }
 
+Py::Object
+RendererAgg::restore_region2(const Py::Tuple& args) {
+  //copy BufferRegion to buffer
+  args.verify_length(7);
+
+
+
+  int x(0),y(0), xx1(0),yy1(0), xx2(0), yy2(0);
+  try {
+xx1 = Py::Int( args[1] );
+yy1 = Py::Int( args[2] );
+xx2 = Py::Int( args[3] );
+yy2 = Py::Int( args[4] );
+x = Py::Int( args[5] );
+y = Py::Int( args[6] );
+  }
+  catch (Py::TypeError) {
+throw Py::TypeError("Invalid input arguments to draw_text_image");
+  }
+
+
+  BufferRegion* region  = static_cast(args[0].ptr());
+
+  if (region->data==NULL)
+throw Py::ValueError("Cannot restore_region from NULL data");
+//return Py::Object();
+
+  //std::cout << "restoring " << region->width << " " << region->height << " " << region->stride << " " << region->rect.x1 << " " << region->rect.y1 << std::endl;
+
+  //agg::rect_i rect((int)l, height - (int)t, (int)r, height - (int)b);
+  //agg::rect_i rect(xx1-region->rect.x1, height - (yy2-region->rect.y1), 
+  //xx2-region->rect.x1, height - (yy1-region->rect.y1));
+  agg::rect_i rect(xx1-region->rect.x1, (yy1-region->rect.y1), 
+		   xx2-region->rect.x1, (yy2-region->rect.y1));
+
+
+  agg::rendering_buffer rbuf;
+  rbuf.attach(region->data,
+	  region->width,
+	  region->height,
+	  regio

Re: [Matplotlib-users] 3rd y-axis in plot

[Jae-Joon Lee]

On Thu, Apr 23, 2009 at 3:54 AM, philscher
 wrote:
>
> Hello,
>
> I need to plot 3 functions into the same plot, each having different scales
> (same x, different y values).
> For the first 2 functions I can use twinx(). But how can I include a 3rd
> axis, which should appear
> beside the first y-axis and plot the 3rd function ?
>

Is this close to what you want?

http://dl.getdropbox.com/u/178748/AxesGrid/htdocs/_images/demo_parasite_axes2.png

If yes, you may take a look at

http://dl.getdropbox.com/u/178748/AxesGrid/htdocs/users/overview.html#axisline

However, it may not work correctly unless you're using the svn version
of the mpl.

-JJ


> Thanks for matplotlib & help
>
> Paul
> --
> View this message in context: 
> http://www.nabble.com/3rd-y-axis-in-plot-tp23174438p23174438.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
>
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Re: [Matplotlib-users] pylab quick reference? (

[Jim Vickroy]

Esmail wrote:

Selam to you too Gökhan,

Gökhan SEVER wrote:
  
What I recommend you is: watching John Hunter's video at Matplotlib by 
John D. Hunter . His 
introduction of matplotlib and examples he use could be very interesting 
to watch for you.



I just started to check out the video, looks interesting and useful,
thanks for the link.
  
I have tried twice to watch this video and each time, after a lengthy 
delay, a "server not found ..." message appears after I click on the 
"play button".  This happens in both Firefox 3 and IE7 on my MS Windows 
XP Pro machine.
  
Also you can take a look at this book: Beginning Python Visualization: 
Crafting Visual Transformation Scripts



I had not heard of this book before, I'll look for more information
on it.

  

Good luck on your plotting adventures.



Thanks - it's fun to learn new things.

Cheers,
Esmail


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Re: [Matplotlib-users] pylab quick reference? (

[Esmail]

Jim Vickroy wrote:
>
> I have tried twice to watch this video and each time, after a lengthy 
> delay, a "server not found ..." message appears after I click on the 
> "play button".  This happens in both Firefox 3 and IE7 on my MS Windows 
> XP Pro machine.

Works here with XP Prof SP2 and Firefox 3.0.9 ... odd.

Esmail


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Re: [Matplotlib-users] pylab quick reference? (

[Gökhan SEVER]

Works here.

Don't know it's a browser issue or something related to your connection.

Best to wait a reply from John Hunter. He might have it uploaded somewhere
else.

And yes developers knows a lot about their product then users. Wish there
were more handy instructional videos -showing step-by-step what is on
throughout the program. I know I am asking too much :)

Gökhan


On Thu, Apr 23, 2009 at 12:40 PM, Jim Vickroy  wrote:

>  Esmail wrote:
>
> Selam to you too Gökhan,
>
> Gökhan SEVER wrote:
>
>
>  What I recommend you is: watching John Hunter's video at Matplotlib by
> John D. Hunter  
> . His
> introduction of matplotlib and examples he use could be very interesting
> to watch for you.
>
>
>  I just started to check out the video, looks interesting and useful,
> thanks for the link.
>
>
>  I have tried twice to watch this video and each time, after a lengthy
> delay, a "server not found ..." message appears after I click on the "play
> button".  This happens in both Firefox 3 and IE7 on my MS Windows XP Pro
> machine.
>
>Also you can take a look at this book: Beginning Python Visualization:
> Crafting Visual Transformation Scripts
>
>
>  I had not heard of this book before, I'll look for more information
> on it.
>
>
>
>  Good luck on your plotting adventures.
>
>
>  Thanks - it's fun to learn new things.
>
> Cheers,
> Esmail
>
>
> --
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
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>
>
>
>
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[Matplotlib-users] 2 simple ??: program exit w/graph, update graph real-time

[Esmail]

Hi,

I have two quick questions:

1. Is it possible to exit a Python program but still have the graph
window generated by pylot remain visible? Right now the program stops
when I display the (only) final graph. When I close this window, the
program exits. I would like to finish the program, but have the graph
stay visible if that's possible (I suppose I could save a graphics
file and then display it - but that's a bit different)

2. Is it possible to update graphs somewhat efficiently during the
runtime of the program? Say I have a loop that generates value to
be plotted. Right now I collect them and plot them at the end, ie

values = []
for i in range(0, 200):
 values.append(i)

various pyplot commands to plot the values list.

I wonder if I could have the graph update during each iteration instead
giving me an up-to-date view of the data. (The above is a super simplified
example of course)

Thanks,
Esmail


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Re: [Matplotlib-users] savefig bug

[Thomas Robitaille]

It works great now - thanks for fixing this!

Thomas

On Apr 23, 2009, at 10:29 AM, Michael Droettboom wrote:

> I think Jae-Joon's assesment is correct, since the logical dpi in PS  
> is hardcoded to 72.0.  I have made this change in the SVN repository.
>
> Mike
>
> Thomas Robitaille wrote:
>> Thanks for your quick reply!
>>
>> I'll be patient and wait for the fix to be made in the SVN  
>> repository,  rather than trying to patch it myself. Do I need to  
>> add any  information to the bug report?
>>
>> Best,
>>
>> Thomas
>>
>> On Apr 21, 2009, at 1:06 PM, Jae-Joon Lee wrote:
>>
>>
>>> I can reproduce this bug with the current svn.
>>>
>>> It works correctly If you set dpi=72, but it seems that it would not
>>> be an option in your case.
>>>
>>> It seems to me that this is related with the change in r6847 that   
>>> Michael made.
>>>
>>> http://matplotlib.svn.sourceforge.net/viewvc/matplotlib/trunk/matplotlib/lib/matplotlib/backends/backend_ps.py?r1=6734&r2=6847
>>>
>>> At line 431 of the backend_ps.py,
>>>
>>>clip = (0.0, 0.0, self.width * self.imagedpi,
>>>  self.height * self.imagedpi)
>>>
>>> I think we should use the dpi of the figure, instead of the imagedpi
>>> of the renderer.
>>> Replacing self.imagedpi with 72 (which is the dpi of the figure when
>>> ps backend is used) seems to solve the problem.
>>>
>>> Thomas, I don't see any easy workaround for this bug other than
>>> patching the code. Others may have better insight though.
>>>
>>> Regards,
>>>
>>> -JJ
>>>
>>>
>>>
>>> On Tue, Apr 21, 2009 at 9:59 AM, Thomas Robitaille
>>>  wrote:
>>>
 Hi,

 I've come across a bug with the savefig method when using the dpi=
 argument and saving an EPS file. If you try the following code, you
 will see that the frame is incomplete. Is there a way to solve this
 from a user point of view?

 ---

 import matplotlib
 matplotlib.use('Agg')
 from matplotlib.pyplot import *

 import numpy as np

 nx,ny = 10,10

 image = np.random.random((nx,ny))

 fig = figure(figsize=(4,4))
 ax = fig.add_subplot(111)
 ax.imshow(image,interpolation='nearest')
 fig.savefig('plot.eps',dpi=30)

 ---

 I've submitted a bug report:

 https://sourceforge.net/tracker/?func=detail&aid=2777476&group_id=80706&atid=560720

 Thanks,

 Thomas

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>>
>>
>> --
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>> Java (TM) technology - register by April 22, and save
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>
> -- 
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> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>


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Re: [Matplotlib-users] Animation with copy_from_bbox / restore_region.

[Elan Pavlov]

Hi Jae-Joon,
Thanks a ton! The problem is actually not the frequency of changes.
The current method uses draw_artist on each update. However, the time
for draw_artist is linear in the *number* of points so for graphs with
a large amount of data it is extremely inefficient. Your patch means
that update time is linear in the amount of data *updated* and not in
the total amount of data.
As for the ticks you have a point. In my application I actually want
ticks to be shifted (as time goes on) so indeed this is what I want.
In general ticks that are shifted out can be redrawn using set_data
methods which are efficient since a tick can be defined as it's
endpoints. Basically when first calling plot() I set all of the tick
locators to Null and then just add ticks as a line (with two points)
based on the desired spacing. Changing a tick location (or if desired
redrawing it in the same location) is basically a call to
set_(x|y)data and then draw_artist for a line with two points (or a
line collection will *slightly* improve performance  if needed).
Anyway, thanks again. I'll play around with it and let you know what I
run into.

Elan
---
I can no other answer make but thanks,
And thanks, and ever thanks.
-- William Shakespeare

On Thu, Apr 23, 2009 at 1:21 PM, Jae-Joon Lee  wrote:
> On Mon, Apr 20, 2009 at 4:34 PM, Elan Pavlov  wrote:
>> Hi,
>>
>> I'm trying to use matplotlib for animating data as it is received from an
>> online source (online in the algorithmic sense not internet:). I'd like
>> the graph plot to be updated with high frequency since the data changes
>> rapidly. I've used the BufferRegion with copy_from_bbox / restore_region
>> and it speeds up the plotting considerably but alas it's still not good
>> enough (with a large number of graphs and a large number of data points in
>> each graph).
>>
>
> Well, if you need your plot updated with very high frequency, MPL may
> not be your tool of choice.
> Anyhow, my first recommendation is not to update the plot frequently.
> I mean, do you have to update the plot for every changes? Can you
> update it every 10th change, for example?
>
>> What I'd like to do is to utilize the fact that the animation is updated
>> in a predictable fashion (i.e., scrolling off the screen to the left as
>> new data arrives) in order to speed up the animation. The idea would be to
>> copy the right 99% of the graph (or some other fraction) via some kind of
>> function similar to copy_from_bbox, move it 1% to the left and then plot
>> the new 1% of the data. The problem is that as far as I can tell the
>> copy_from_bbox/restore_region does not actually allow changing the area in
>> which it is restored. I've mucked around in the source files a bit but to
>> no avail.
>>
>> My question is then:
>> 1. Is there some other way to copy everything enclosed in a Bbox? or
>> 2. Is there some way to modify the region in which data reappears when
>> using restore_region?
>> 3. Perhaps I'm missing something?
>>
>> I'm sure someone else has done this since it seems pretty natural and
>> useful for a variety of applications.
>
> I'm attaching a patch that might do what you want to do.
> It implements a "restore_bbox2" method which restores a subset of the
> saved background at a specified position.
> A small example is also attached (it is based on the gtk backend).
>
> I, personally, am not sure if this kind of feature is useful. If you
> shift part of your figure, you have to be careful not to mess up with
> the coordinate system. And also be careful about what to be shifted
> and what to be not (e.g., ticks).
>
> If others find this useful, I'll commit this to the trunk with some
> api improvement.
>
> Regards,
>
> -JJ
>
>
>>
>> Elan
>> 
>> "If stupidity got us into this mess, why can't it get us out?"
>>        - Will Rogers
>>
>> --
>> Stay on top of everything new and different, both inside and
>> around Java (TM) technology - register by April 22, and save
>> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
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>> Use priority code J9JMT32. http://p.sf.net/sfu/p
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>>
>
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>



-

[Matplotlib-users] How to maximaze a Tkinter window

[Coert Klaver]

Hi,

I would like to maximize a window that is generated by pyplot.

Example code:

import numpy as np
import matplotlib.pyplot as plt

t = np.arange(0., 5., 0.2)
line, = plt.plot(t, t**2, 'bo')
plt.show()

I found code on how to do this in Tkinter mailing:


def maximize_toplevel( widget ):
 toplevel = root.winfo_toplevel()

 try:
 # On MS Windows one can set the "zoomed" state.
 toplevel.wm_state( 'zoomed' )
 except:
 w = root.winfo_screenwidth()
 h = root.winfo_screenheight() - 60

 geom_string = "%dx%d+0+0" % (w,h)
 toplevel.wm_geometry( geom_string )
 return

But I have no clue how to apply this in the pyplot environment. In 
other words, how do I get from the plt.show() call to something that 
can be passed to the maximize_toplevel function?

Thanks for any hint

UV 


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Re: [Matplotlib-users] 2 simple ??: program exit w/graph, update graph real-time

[Ryan May]

On Thu, Apr 23, 2009 at 1:04 PM, Esmail  wrote:

> Hi,
>
> I have two quick questions:
>
> 1. Is it possible to exit a Python program but still have the graph
> window generated by pylot remain visible? Right now the program stops
> when I display the (only) final graph. When I close this window, the
> program exits. I would like to finish the program, but have the graph
> stay visible if that's possible (I suppose I could save a graphics
> file and then display it - but that's a bit different)
>
> 2. Is it possible to update graphs somewhat efficiently during the
> runtime of the program? Say I have a loop that generates value to
> be plotted. Right now I collect them and plot them at the end, ie
>
> values = []
> for i in range(0, 200):
> values.append(i)
>
> various pyplot commands to plot the values list.
>
> I wonder if I could have the graph update during each iteration instead
> giving me an up-to-date view of the data. (The above is a super simplified
> example of course)


Try this:

http://matplotlib.sourceforge.net/examples/animation/simple_anim_gtk.html

(If not gtk, there are other examples there.)

Ryan

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Re: [Matplotlib-users] 2 simple ??: program exit w/graph, update graph real-time

[Esmail]

Ryan May wrote:
> 
> Try this:
> 
> http://matplotlib.sourceforge.net/examples/animation/simple_anim_gtk.html
> 
> (If not gtk, there are other examples there.)

Thanks Ryan, that'll give me some idea with regard to the animation,
and real-time drawings.

Any idea if it's possible to finish a Python program but still have the
graph showing?

FWIW, I'm doing this under Linux.

Thanks,
Esmail


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[Matplotlib-users] setting hist(log=True) causes recursion depth to be exceeded

[AugustineDunn]

Hello,

I am sorry if this gets double posted but it has spent more than a day in
mailing-list limbo!

I have been trying to plot a hist of a large data array (len ~ 15,000) and
the log=True switch causes the following error to be thrown:

RuntimeError: Maximum recursion depth exceeded
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/transforms.py",
line 87, in __init__
  self._parents = WeakKeyDictionary()

It works fine when i try it on smaller test data sets.  When I use
sys.setrecursionlimit() to many values it either still exceeds max depth or
blows its mind and dies.  Is there any way to do this without MAJOR code
length increases?

Thanks. 
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Re: [Matplotlib-users] 2 simple ??: program exit w/graph, update graph real-time

[Ryan May]

On Thu, Apr 23, 2009 at 4:16 PM, Esmail  wrote:

> Ryan May wrote:
> >
> > Try this:
> >
> >
> http://matplotlib.sourceforge.net/examples/animation/simple_anim_gtk.html
> >
> > (If not gtk, there are other examples there.)
>
> Thanks Ryan, that'll give me some idea with regard to the animation,
> and real-time drawings.
>
> Any idea if it's possible to finish a Python program but still have the
> graph showing?
>
> FWIW, I'm doing this under Linux.
>

You'd have to run the plotting in a separate process from the computation.
subprocess would let you do that, assuming you can spin off a child task
that stays alive when the parent exits.  You'd also need to get the
computing process to give new results to the child plot, maybe using a pipe
(which I think subprocess can handle as well.)

Ryan

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Re: [Matplotlib-users] Matplotlib on OS X 10.4 (was: can't import pylab)

[John Seales]

I've been using python 2.6 for several months. I can't remember how I installed 
it. 
Matplotlib is from sourceforge. Filename: matplotlib-0.98.5.2-py2.5-mpkg.zip.



> To: matplotlib-users@lists.sourceforge.net
> From: j...@iki.fi
> Date: Tue, 21 Apr 2009 10:10:10 +0300
> Subject: [Matplotlib-users] Matplotlib on OS X 10.4 (was: can't import pylab)
> 
> John Seales  writes:
> 
> > I'm using Mac os 10.4.11. Python is included in mac os. 
> 
> The error messages refer to Python 2.6:
> 
> >> > ImportError: 
> >> > dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/ft2font.so,
> >> >  2): Library not loaded: /usr/X11R6/lib/libfreetype.6.dylib
> >> >   Referenced from: 
> >> > /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/ft2font.so
> 
> If you are somehow using this with the system Python, it's no wonder
> that you are having problems. I think OS X 10.4 includes Python 2.3 or
> at most 2.4 - version 10.5 has Python 2.5. But perhaps you have
> installed some other version of Python - one way to test what you are
> using is to look at where Python gets its modules:
> 
> ~% python
> Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) 
> [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import os
> >>> os
>  '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/os.pyc'>
> 
> (So I am using something else than the system-supplied Python, whose
> os.pyc file is under /System/Library.)
> 
> Some distributions of Python for OS X are mentioned here:
> http://matplotlib.sourceforge.net/faq/installing_faq.html#which-python-for-osx
> 
> > Matplotlib I installed from a precompiled version.
> 
> Is this the version from Sourceforge, or somewhere else?
> 
> Anyway, the library linking problems sound a lot like you are using
> software that was not compiled for your version of OS X - I guess most
> developers have upgraded to Leopard quite some time ago, so they would
> not notice if something breaks on older releases.
> 
> The larger question is, which versions of OS X should be supported by
> the binary packages? The ReadMe.txt bundled with the MacPython 2.6.2
> installer says:
> 
> This package will install MacPython 2.6.2 for Mac OS X
> 10.3 or later for the following 
> architecture(s): i386, ppc.
> 
> So Python itself supports Panther and newer, and I think the compiler
> flags used by Python are inherited by extensions - but if there is
> something other than just compiler flags to worry about, someone would
> have to have an installation of the target version of OS X to test on. 
> 
> -- 
> Jouni K. Seppänen
> http://www.iki.fi/jks
> 
> 
> --
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[Matplotlib-users] Segmentation fault using imshow on large image

[Adam Ginsburg]

Hi, I've been getting a segmentation fault when trying to display
large images.  A transcript of a sample session is below.  I'm using
the TkAgg backend, and I am using numpy, but otherwise I have made no
modifications to the matplotlib setup.


milkyway /data/glimpseii $ alias pylab
alias pylab='/usr/local/adm/config/python/bin/ipython -pylab -log'
milkyway /data/glimpseii $ pylab
Activating auto-logging. Current session state plus future input saved.
Filename   : ipython_log.py
Mode   : rotate
Output logging : False
Raw input log  : False
Timestamping   : False
State  : active
Python 2.5 (r25:51908, Dec 22 2006, 16:08:43)
Type "copyright", "credits" or "license" for more information.

IPython 0.9.1 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help  -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

  Welcome to pylab, a matplotlib-based Python environment.
  For more information, type 'help(pylab)'.

In [1]: import matplotlib,pyfits,numpy,scipy

In [2]: scipy.__version__
Out[2]: '0.7.0'

In [3]: numpy.__version__
Out[3]: '1.3.0'

In [4]: matplotlib.__version__
Out[4]: '0.98.5.2'

In [5]: f = pyfits.open('GLM_00600+_mosaic_I3.fits')

In [6]: f[0].data.shape
Out[6]: (10370, 9320)

In [7]: f[0].data.dtype
Out[7]: dtype('>f4')

In [8]: imshow(f[0].data)
Segmentation fault


Any ideas?

Thanks,
Adam

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Re: [Matplotlib-users] Matplotlib on OS X 10.4

[Jouni K . Seppänen]

John Seales  writes:

> I've been using python 2.6 for several months. I can't remember how I 
> installed it. 
> Matplotlib is from sourceforge. Filename: matplotlib-0.98.5.2-py2.5-mpkg.zip.

That package only works with Python 2.5 (hence "py2.5" in the file
name). If you somehow managed to install it into your Python 2.6
hierarchy, that would explain the strange error messages.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks


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